I think they'd be treated as separate except in cases where the connection between them is relevant.

So a Dracula badfic obviously wouldn't benefit at all from a copy of one of the video games, but a Castlavania badfic might from a copy of the book. However, I'd say that in the latter case, it'd probably not be very effective unless the fic specifically violated the part of Castlevania canon that's supposed to be covered by Dracula.

I guess. >.

I think that the Dracula story is the Canon. Castlevania is an offshoot of the Dracula legend, like the branch of a tree. In this case, it seems more like the offshoot is trying to become more true to the original Canon.

To sum up, they are both Canon, but I would call Castlevania a child-Canon to Stoker's parent-Canon. The good news is that you can definitely use a copy of the book to exorcise a Castlevania fic.

I think that if you have two canons that are connected, with or without actual interaction, then they are actually part of the same root canon. That canon may not have a name, but I think it still exists.